Well, I believe that it's actually less confusing like this.
The customer can see in the cart that there is a shipping fee in the cart, then, he adds the coupon for free shipping, and then the cart displays the shipping fee, plus the coupon removing the same amount as the shipping fee.
So to me it's not a "bug that needs to be fixed". It's working like how it was designed to work.
Now could it work differently ? It's technically possible. So far however, you're the first one talking about this being a problem so we would need more inputs before changing such a thing or making it an option.